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v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian
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@apeltzer apeltzer released this 23 Feb 11:00
· 460 commits to master since this release
2.3.0
c611b15
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Learn about vigilant mode.

v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian

  • [#307] - Clean up config file and improve output folder structure
  • [#299] - Bugfix for missing inputs in BAM stats (genome_quant.r)
  • [#164] - UMI Handling Feature implemented in the pipeline
  • [#302] - Merged in nf-core template v2.11.1
  • [#294] - Fixed contamination screening issues
  • [#309] - Merged in nf-core template v2.12.0
  • [#310] - Removed unnecessarily separate mirtrace subworkflow, now using module instead
  • [#311] - Fix use of FASTP, set three_prime_adapter per default
  • [#314] - Add parameters to control publishing of intermediate results
  • [#317] - Fixed issue with bowtie indices directly supplied
  • [#318] - Merged in nf-core template v2.13.0 and pinned nf-validator

Parameters

Old parameter New parameter
--with_umi
--umitools_extract_method
--umitools_method
--skip_umi_extract
--umitools_bc_pattern
--umi_discard_read
--save_umi_intermeds
--save_aligned
--save_aligned_mirna_quant
--save_merged

Software dependencies

Dependency Old version New version
multiqc 1.15 1.20
edgeR 3.36.0 4.0.2
limma 3.50.0 3.58.1
bioconvert 0.4.3 1.1.1
mirdeep 2.0.1 2.0.1.3
seqkit 2.3.1 2.6.1
fastqc 0.11.4 0.12.1
samtools 1.17 1.19.2
umitools 1.1.5
umicollapse 1.0.0
Assets 2
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